Parent Child and Mix 'n Match

I have a client who has put into place Parent and Child items. They sell either the box or a bar for which the system works perfectly at managening the inventory. Where things go wrong is when they use Mix and Match in combination to Parent and Child. For some reason the system no longer works, the situtaion is that if you buy a combination of different flavor of bars and buy the same amount as in a box, you get the box price, but the inventory levels no longer work properly as they did before. Is there a work around or a fix for this?